Hi,
This is the output after running parmed.py as suggested:-
-------------------------------------------------------------
Loaded Amber topology file pk.prmtop
Reading input from STDIN...
> Loading restart file pk.inpcrd
> Amino Acid Residues: 0
Nucleic Acid Residues: 23
Number of cations: 20
Number of anions: 0
Num. of solvent mols: 36479
Num. of unknown atoms: 3
Total charge (e-): -0.2183
Total mass (amu): 666024.8380
Number of atoms: 110301
Number of residues: 36525
System volume (ang^3): 1275508.533652
System density (g/mL): 0.867088
> Done!
-------------------------------------------------------------
The problem that i mentioned before occurs even when i solvate using the
usual solvatebox command (solvatebox mol TIP3PBOX 30). Interestingly, when
i played around with different values, setting a value >20 (for
solvatebox) started giving this problem.
My purpose is to generate a water box which has a larger dimension in z
direction (for SMD), hence i used {30 30 45}.
Thanks
Asmita
On Sun, Apr 26, 2015 at 2:10 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sat, Apr 25, 2015 at 11:37 AM, Asmita Gupta <asmita4des.gmail.com>
> wrote:
>
> > Dear users,
> >
> > I have prepared a system using following leap commands:
> >
> > verbosity 2
> > loadamberparams frcmod.ionsjc_tip3p
> > mol=loadpdb pk_aligned.pdb
> > addions mol Na+ 0
> > solvatebox mol TIP3PBOX {30 30 45}
> > saveamberparm mol pk.prmtop pk.inpcrd
> >
> > i minimized the structure, heated it to 300k and ran equilibration for 2
> > ns. At each step, i checked the structure for presence of any close
> > contacts using "check" command.
> >
> > After minimization and heating, the system didn't report any close
> contacts
> > but after equilibration, i got a long list of close contacts (both
> between
> > solute-solvent and solvent-solvent) like this:-
> >
> > --------------------------------------------------------------------
> > 1 Warning: Atoms 4:C5_1.H5' and 66330:WAT_21868.H2 are close (0.67)
> > 1 Warning: Atoms 13:C5_1.H6 and 20392:WAT_6556.O are close (0.34)
> > 1 Warning: Atoms 13:C5_1.H6 and 20394:WAT_6556.H2 are close (0.69)
> > 1 Warning: Atoms 30:G_2.P and 87424:WAT_28900.O are close (0.71)
> > 1 Warning: Atoms 30:G_2.P and 87425:WAT_28900.H1 are close (0.26)
> > 1 Warning: Atoms 37:G_2.C4' and 10084:WAT_3120.O are close (0.67)
> > 1 Warning: Atoms 37:G_2.C4' and 10085:WAT_3120.H1 are close (0.63)
> > 1 Warning: Atoms 42:G_2.N9 and 32186:WAT_10487.H1 are close (0.77)
> > 1 Warning: Atoms 43:G_2.C8 and 32186:WAT_10487.H1 are close (0.58)
> > .
> > .
> > .
> > .
> > --------------------------------------------------------------------
> >
> > What's going wrong here?
> >
>
> Using the prmtop and inpcrd files you got from leap, run the following
> command in ParmEd:
>
> parmed.py -p pk.prmtop << EOF
>
> loadRestrt pk.inpcrd
>
>
> summary
> EOF
>
> What is the output of this command? I'm particularly interested in the
> reported density. I've never actually solvated the way you did (i.e.,
> explicitly setting the box dimensions), so I wonder if the PBC were not set
> particularly well (an overly high density would explain your observations).
>
> Also, I suggest using the "addIons" command *after* solvating, so that
> water molecules are replaced by ions (or use "addIonsRand" instead, which
> results in a more random ion distribution to start with).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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>
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Received on Sat Apr 25 2015 - 15:00:02 PDT
